As best I can tell the "missing" plug-ins are DX format.
DX plug-ins do not rely on users defining paths to their locations. DX plug-ins are registered during installation. Moving them to a VST folder will not help, in fact that will break the ability of SONAR to find them since SONAR relies on the information placed in the registry during installation.
Running the VST scanner will not help, it does not work with DX plug-ins.
While SONAR installers will update plug-ins and utilities, the installers do not remove them.
Since the plug-ins work in existing projects, this would suggest the plug-ins are installed correctly and SONAR can find them. It seems like the plug-ins are missing for the current layout. Is the plug-in layout set to "Default all plug-ins?"